The business miles you drove are still considered business miles whether or not you are reimbursed for some of them.
As an independent contractor, the reimbursement you receive is considered to be 'other' income for your business. You would include the miles as business miles and deduct any expenses based on your percent of business use. These deductions will help to offset the additional income you received as mileage reimbursement. Claiming actual expenses, you may break even based on the reimbursement or have some extra income or extra deductions depending on your total vehicle expenses.
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